No, he quotes a study by Greg Winter where 10-100 million sites needed to be provided in order to give a match for a new site.
That’s partly the study I mentioned above, and partly reasoning about protein shape space. It’s several pages long.
Speaking of Winter’s work, Behe writes “In all of these experiments, mutations were deliberately confined to a coherent patch of amino acids that were close to each other on the surface of the protein, to make as many novel, binding-site-sized regions as possible. If the workers had not deliberately directed the changes to a coherent patch on the protein’s surface, most changes would be scattered, unable to effectively interact.” (p. 132)
Well, yes, we’re looking for the probability of a given binding site to develop, that is a probability of interest, and a reasonable objective.
Because “that would be an event of approximately the right frequency.”
And Behe acknowledges that: “between ten and a hundred million binding sites have to be searched in a shape space library to find one that will bind with a modest affinity to a second protein.” (p. 273)
“12.As discussed in Chapter 7, there are different kinds of mutations—deletions, duplications, and so on. But point mutation represents the conceptually simplest, most straightforward route. This calculation uses consensus values for important variables. One could certainly imagine other scenarios for making a new protein-binding site, for example by first invoking gene duplication and then point mutation. But those are either unlikely to help much (Behe, M. J., and Snoke, D. W. 2004. Simulating evolution by gene duplication of protein features that require multiple amino acid residues. Protein Sci. 13:2651–64) or likely to involve special circumstances that amount to a Just-So story. All alternative scenarios would have to confront the fact that no new binding sites have turned up in the best-studied evolutionary cases of malaria and HIV, as described later in the text.”
13.Even though protein-binding sites often involve a score of amino acids on each of the partners, experiments have shown that only a fraction of those are important for having the two proteins stick to each other. (For example, see Braden, B. C., and Poljak, R. J. 1995. Structural features of the reactions between antibodies and protein antigens. FASEB J. 9:9–16; Lo Conte, L., Chothia, C., and Janin, J. 1999. The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285:2177–98; Ma, B., Elkayam, T., Wolfson, H., and Nussinov, R. 2003. Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc. Natl. Acad. Sci. USA 100:5772–77.) In terms of the swimming pool analogy, the five or six residues represent bumps and magnets that are aligned very nicely; if enough are aligned, then it doesn’t matter so much if other features aren’t aligned, as long as they don’t actively block the surfaces from coming together."